3CSK

Structure of DPP III from Saccharomyces cerevisiae

Summary for 3CSK

• Entry DOI: 10.2210/pdb3csk/pdb
• Descriptor: Probable dipeptidyl-peptidase 3, ZINC ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: zn-hydrolase, aminodipeptidase, hexxgh-motif, aminopeptidase, hydrolase, metal-binding, metalloprotease, protease
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Cytoplasm (Probable): Q08225
• Total number of polymer chains: 1
• Total formula weight: 80763.21

Authors

Baral, P.K.,Jajcanin, N.,Deller, S.,Macheroux, P.,Abramic, M.,Gruber, K. (deposition date: 2008-04-10, release date: 2008-06-10, Last modification date: 2024-05-29)

Primary citation

Baral, P.K.,Jajcanin-Jozic, N.,Deller, S.,Macheroux, P.,Abramic, M.,Gruber, K.
The first structure of dipeptidyl-peptidase III provides insight into the catalytic mechanism and mode of substrate binding.
J.Biol.Chem., 283:22316-22324, 2008

PubMed Abstract: Dipeptidyl-peptidases III (DPP III) are zinc-dependent enzymes that specifically cleave the first two amino acids from the N terminus of different length peptides. In mammals, DPP III is associated with important physiological functions and is a potential biomarker for certain types of cancer. Here, we present the 1.95-A crystal structure of yeast DPP III representing the prototype for the M49 family of metallopeptidases. It shows a novel fold with two domains forming a wide cleft containing the catalytic metal ion. DPP III exhibits no overall similarity to other metallopeptidases, such as thermolysin and neprilysin, but zinc coordination and catalytically important residues are structurally conserved. Substrate recognition is accomplished by a binding site for the N terminus of the peptide at an appropriate distance from the metal center and by a series of conserved arginine residues anchoring the C termini of different length substrates.

PubMed: 18550518
DOI: 10.1074/jbc.M803522200

Experimental method

X-RAY DIFFRACTION (1.95 Å)